7976e2588e92dca0567231cf3998759bf6f1827f max Thu May 7 03:27:42 2015 -0700 implementing the external tools "send to" menu, refs #15113 diff --git src/hg/hgTracks/menu.c src/hg/hgTracks/menu.c index deaa91b..56af8bd 100644 --- src/hg/hgTracks/menu.c +++ src/hg/hgTracks/menu.c @@ -1,372 +1,448 @@ // Code to create hgTracks menu bar /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "dystring.h" #include "ensFace.h" #include "agpFrag.h" #include "ctgPos.h" #include "hCommon.h" #include "htmshell.h" #include "hash.h" #include "liftOver.h" #include "wikiLink.h" #include "web.h" #include "geoMirror.h" #include "hgTracks.h" #include "trackHub.h" +#include "extTools.h" /* list of links to display in a menu */ struct hotLink { struct hotLink *next; char *name; char *url; char *id; + char *mouseOver; + boolean inactive; /* greyed out */ boolean external; }; static void appendLink(struct hotLink **links, char *url, char *name, char *id, boolean external) { // append to list of links for later printing and/or communication with javascript client struct hotLink *link; AllocVar(link); link->name = cloneString(name); link->url = cloneString(url); link->id = cloneString(id); link->external = external; +link->inactive = FALSE; slAddTail(links, link); } +static void appendLinkMaybeInactive(struct hotLink **links, char *url, char *name, char *id, + boolean external, boolean inactive) +{ +appendLink(links, url, name, id, external); +struct hotLink *le = slLastEl(links); +le->inactive=inactive; +} + static void printEnsemblAnchor(char *database, char* archive, char *chrName, int start, int end, struct hotLink **links) /* Print anchor to Ensembl display on same window. */ { char *scientificName = hScientificName(database); char *dir = ensOrgNameFromScientificName(scientificName); struct dyString *ensUrl; char *name; int localStart, localEnd; name = chrName; if (sameWord(scientificName, "Takifugu rubripes")) { /* for Fugu, must give scaffold, not chr coordinates */ /* Also, must give "chrom" as "scaffold_N", name below. */ if (differentWord(chromName,"chrM") && !hScaffoldPos(database, chromName, winStart, winEnd, &name, &localStart, &localEnd)) /* position doesn't appear on Ensembl browser. * Ensembl doesn't show scaffolds < 2K */ return; } else if (sameWord(scientificName, "Gasterosteus aculeatus")) { if (differentWord("chrM", chrName)) { char *fixupName = replaceChars(chrName, "chr", "group"); name = fixupName; } } else if (sameWord(scientificName, "Ciona intestinalis")) { if (stringIn("chr0", chrName)) { char *fixupName = replaceChars(chrName, "chr0", "chr"); name = fixupName; } } else if (sameWord(scientificName, "Saccharomyces cerevisiae")) { if (stringIn("2micron", chrName)) { char *fixupName = replaceChars(chrName, "2micron", "2-micron"); name = fixupName; } } if (sameWord(chrName, "chrM")) name = "chrMt"; ensUrl = ensContigViewUrl(database, dir, name, seqBaseCount, start+1, end, archive); appendLink(links, ensUrl->string, "Ensembl", "ensemblLink", TRUE); /* NOTE: you can not freeMem(dir) because sometimes it is a literal * constant */ freeMem(scientificName); dyStringFree(&ensUrl); } static void fr2ScaffoldEnsemblLink(char *archive, struct hotLink **links) /* print out Ensembl link to appropriate scaffold there */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr = NULL; char **row = NULL; char query[256]; sqlSafef(query, sizeof(query), "select * from chrUn_gold where chrom = '%s' and chromStart<%u and chromEnd>%u", chromName, winEnd, winStart); sr = sqlGetResult(conn, query); int itemCount = 0; struct agpFrag *agpItem = NULL; while ((row = sqlNextRow(sr)) != NULL) { agpFragFree(&agpItem); // if there is a second one agpItem = agpFragLoad(row+1); ++itemCount; if (itemCount > 1) break; } sqlFreeResult(&sr); hFreeConn(&conn); if (1 == itemCount) { // verify *entirely* within single contig if ((winEnd <= agpItem->chromEnd) && (winStart >= agpItem->chromStart)) { int agpStart = winStart - agpItem->chromStart; int agpEnd = agpStart + winEnd - winStart; printEnsemblAnchor(database, archive, agpItem->frag, agpStart, agpEnd, links); } } agpFragFree(&agpItem); // the one we maybe used } +void freeLinksAndConvert(struct hotLink *links, struct dyString *menuHtml) +/* convert the links to html strings and append to the dyString "menu", destroying the links */ +{ +int len = slCount(links); +int i = 0; +struct hotLink *link = NULL; +for(i = 0, link = links; link != NULL; i++, link = link->next) + { + char class[100]; + if(i == 0) + safef(class, sizeof(class), "first"); + else if (i + 1 == len) + safef(class, sizeof(class), "last"); + else + class[0] = 0; + dyStringAppend(menuHtml, "<li"); + char *encodedName = htmlEncode(link->name); + if(*class) + dyStringPrintf(menuHtml, " class='%s'", class); + dyStringPrintf(menuHtml, "><a href='%s' id='%s'%s>%s</a></li>\n", link->url, link->id, + link->external ? " TARGET='_blank'" : "", encodedName); + freez(&encodedName); + + freez(&link->name); + freez(&link->url); + freez(&link->id); + } +slFreeList(links); +} + +static void addSendToMenuItems(struct dyString *viewMenu, char* uiVars) +/* add the "send to" menu to the "viewMenu" dyString */ +{ +struct hotLink *viewLinks = NULL; + +char url[4096]; +char label[4096]; + +struct extTool *extTools = readExtToolRa("extTools.ra"); +struct extTool *et; +for(et = extTools; et != NULL; et = et->next) + { + if (et->dbs!=NULL) + { + if (!slNameInList(et->dbs, database)) + continue; + } + if (et->params==NULL) + { + char *replUrl = replaceInUrl(et->url, "", cart, database, chromName, winStart, winEnd, NULL, TRUE); + safef(url, sizeof(url), "%s", replUrl); + //safef(url, sizeof(url), "%s %s", chromName, database); + } + else + safef(url, sizeof(url), "hgTracks?%s&hgt.redirectTool=%s", uiVars, et->tool); + boolean inactive = FALSE; + if (et->maxSize!=0) + { + inactive = TRUE; + if (et->maxSize>1000) + safef(label, sizeof(label), "%s (< %d kbp)", et->shortLabel, et->maxSize/1000); + else + safef(label, sizeof(label), "%s (< %d bp)", et->shortLabel, et->maxSize); + } + else + safef(label, sizeof(label), "%s", et->shortLabel); + + appendLinkMaybeInactive(&viewLinks, url, label, "extTool", TRUE, inactive); + } + +freeLinksAndConvert(viewLinks, viewMenu); + +} + void printMenuBar() /* Put up the menu bar. */ { -struct hotLink *link, *links = NULL; -int i, len; +struct hotLink *links = NULL; struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = hAllocConn(database); char *menuStr, buf[4096], uiVars[1024]; safef(uiVars, sizeof(uiVars), "%s=%s", cartSessionVarName(), cartSessionId(cart)); menuStr = menuBar(cart, database); // Create top items in view menu safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.psOutput=on", uiVars); appendLink(&links, buf, "PDF/PS", "pdfLink", FALSE); safef(buf, sizeof(buf), "%s&o=%d&g=getDna&i=mixed&c=%s&l=%d&r=%d&db=%s&%s", hgcNameAndSettings(), winStart, chromName, winStart, winEnd, database, uiVars); appendLink(&links, buf, "DNA", "dnaLink", FALSE); safef(buf, sizeof(buf), "../cgi-bin/hgConvert?hgsid=%s&db=%s", cartSessionId(cart), database); appendLink(&links, buf, "in other Genomes (Convert)", "convertMenuLink", FALSE); // Add link-outs to other dbs as appropriate for this assembly if (differentWord(database,"susScr2")) { /* Print Ensembl anchor for latest assembly of organisms we have * supported by Ensembl == if versionString from trackVersion exists */ char ensVersionString[256], ensDateReference[256]; ensGeneTrackVersion(database, ensVersionString, ensDateReference, sizeof(ensVersionString)); if ((conn != NULL) && sqlTableExists(conn, UCSC_TO_ENSEMBL)) printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links); else if (sameWord(database,"hg19")) { printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links); } else if (sameWord(database,"hg18")) { printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd, &links); } else if (sameWord(database,"oryCun2") || sameWord(database,"anoCar2") || sameWord(database,"calJac3")) { printEnsemblAnchor(database, NULL, chromName, winStart, winEnd, &links); } else if (ensVersionString[0]) { char *archive = NULL; if (ensDateReference[0] && differentWord("current", ensDateReference)) archive = cloneString(ensDateReference); /* Can we perhaps map from a UCSC random chrom to an Ensembl contig ? */ if (isUnknownChrom(database, chromName)) { // which table to check char *ctgPos = "ctgPos"; if (sameWord(database,"fr2")) fr2ScaffoldEnsemblLink(archive, &links); else if (hTableExists(database, UCSC_TO_ENSEMBL)) printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links); else if (hTableExists(database, ctgPos)) /* see if we are entirely within a single contig */ { struct sqlResult *sr = NULL; char **row = NULL; char query[256]; sqlSafef(query, sizeof(query), "select * from %s where chrom = '%s' and chromStart<%u and chromEnd>%u", ctgPos, chromName, winEnd, winStart); sr = sqlGetResult(conn, query); int itemCount = 0; struct ctgPos *ctgItem = NULL; while ((row = sqlNextRow(sr)) != NULL) { ctgPosFree(&ctgItem); // if there is a second one ctgItem = ctgPosLoad(row); ++itemCount; if (itemCount > 1) break; } sqlFreeResult(&sr); if (1 == itemCount) { // verify *entirely* within single contig if ((winEnd <= ctgItem->chromEnd) && (winStart >= ctgItem->chromStart)) { int ctgStart = winStart - ctgItem->chromStart; int ctgEnd = ctgStart + winEnd - winStart; printEnsemblAnchor(database, archive, ctgItem->contig, ctgStart, ctgEnd, &links); } } ctgPosFree(&ctgItem); // the one we maybe used } } else { printEnsemblAnchor(database, archive, chromName, winStart, winEnd, &links); } } } hFreeConn(&conn); if (sameString(database, "hg38")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "hg19")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&build=previous&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "mm8")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "danRer2")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7955&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "galGal3")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "canFam2")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9615&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "rheMac2")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9544&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "panTro2")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9598&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "anoGam1")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7165&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (sameString(database, "bosTau6")) { safef(buf, sizeof(buf), "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9913&CHR=%s&BEG=%d&END=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "NCBI", "ncbiLink", TRUE); } else if (startsWith("oryLat", database)) { safef(buf, sizeof(buf), "http://medaka.utgenome.org/browser_ens_jump.php?revision=version1.0&chr=chromosome%s&start=%d&end=%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "UTGB", "medakaLink", TRUE); } else if (sameString(database, "cb3")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/seq/gbrowse/briggsae?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } else if (sameString(database, "cb4")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_briggsae?name=%s:%d-%d", chromName, winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } else if (sameString(database, "ce10")) { safef(buf, sizeof(buf), "http://www.wormbase.org/db/gb2/gbrowse/c_elegans?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } else if (sameString(database, "ce4")) { safef(buf, sizeof(buf), "http://ws170.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } else if (sameString(database, "ce2")) { safef(buf, sizeof(buf), "http://ws120.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d", skipChr(chromName), winStart+1, winEnd); appendLink(&links, buf, "WormBase", "wormbaseLink", TRUE); } // finish View menu safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgTracksConfigPage=configure", uiVars); appendLink(&links, buf, "Configure Browser", "configureMenuLink", FALSE); safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.reset=on", uiVars); appendLink(&links, buf, "Default Tracks", "defaultTracksMenuLink", FALSE); safef(buf, sizeof(buf), "../cgi-bin/hgTracks?%s&hgt.defaultImgOrder=on", uiVars); appendLink(&links, buf, "Default Track Order", "defaultTrackOrderMenuLink", FALSE); appendLink(&links, "../cgi-bin/cartReset", "Reset all user settings", "cartResetMenuLink", FALSE); struct dyString *viewMenu = dyStringCreate("<li class='menuparent' id='view'><span>View</span>\n<ul style='display: none; visibility: hidden;'>\n"); -len = slCount(links); -for(i = 0, link = links; link != NULL; i++, link = link->next) +freeLinksAndConvert(links, viewMenu); +dyStringAppend(viewMenu, "</ul>\n</li>\n"); + +// add the sendTo menu +if (fileExists("extTools.ra")) { - char class[100]; - if(i == 0) - safef(class, sizeof(class), "first"); - else if (i + 1 == len) - safef(class, sizeof(class), "last"); - else - class[0] = 0; - char *encodedName = htmlEncode(link->name); - dyStringAppend(viewMenu, "<li"); - if(*class) - dyStringPrintf(viewMenu, " class='%s'", class); - dyStringPrintf(viewMenu, "><a href='%s' id='%s'%s>%s</a></li>\n", link->url, link->id, - link->external ? " TARGET='_blank'" : "", encodedName); - freez(&encodedName); - } + dyStringAppend(viewMenu, "<li class=\"menuparent\" id=\"sendTo\"><span>Send To</span><ul>"); + addSendToMenuItems(viewMenu, uiVars); dyStringAppend(viewMenu, "</ul>\n</li>\n"); + } menuStr = replaceChars(menuStr, "<!-- OPTIONAL_VIEW_MENU -->", dyStringCannibalize(&viewMenu)); hPuts(menuStr); freez(&menuStr); }